13. 2. Values

Depending on the context, an expression can use values of a data item. If an expression is evaluated for a data item, it can use the values of this item. E. g. an expression that is an argument of a command that operates on atoms can use the values of this atom, like its name. The following is a table of the values that are valid for each data item:

item	value	type	explanation
`mol`	`num`	integer	molecule number
`mol`	`number`	integer	molecule number
`res`	`num`	integer	residue number
`res`	`number`	integer	residue number
`prim`	`num`	integer	primary number
`prim`	`number`	integer	primary number
`mol`	`name`	string	molecule name
`res`	`name`	string	residue name
`atom`	`name`	string	atom name
`angle`	`name`	string	angle name
`atom`	`shift`	float	chemical shift of atom
`atom`	`bfactor`	float	B factor of atom
`atom`	`vdw`	float	van der Waals radius of atom
`atom`	`charge`	float	partial charge of atom
`atom`	`heavycharge`	float	charges on heavy atoms
`atom`	`avgcharge`	float	averaged charges on heavy atoms
`atom`	`simplecharge`	float	simple charges from setup file
`atom`	`d`	float	distance from reference atom(s)
`angle`	`val`	float	angle
`dist`	`val`	float	distance
`dist`	`limit`	float	limit of constraint
`dist`	`viol`	float	violation of constraint
`dist`	`upl`	bool	true if distance is upper limit
`dist`	`lol`	bool	true if distance is lower limit
`dist`	`hbond`	bool	true if distance is H-bond
`atom`	`attr`	integer	graphics attribute index
`bond`	`attr`	integer	graphics attribute index
`dist`	`attr`	integer	graphics attribute index
`prim`	`attr`	integer	graphics attribute index

Values of an item can be referenced by just using their name. It is also possible to access values of items that are higher in the data hierarchy. This is done in the form item.value, e. g. res.name in an expression that is evaluated for an atom. The following figure shows the data hierarchy:

Not all primitives belong to a molecule. For the ones that do not (titles), accessing molecule values will result in null values (0 for the number, empty string for the name).

For bonds, distances and angles, it is also possible to access the values of the atoms involved. For bonds this is done by using the items atom1 and atom2, for dihedral angles the 4 atoms defining it can be accessed over atom1, atom2, atom3, and atom4.

For bonds and distances, it is also possible to access the values of both residues involved. This is done by using the items res1 and res2.

For distances, it is also possible to access the values of both molecules involved. This is done by using the items mol1 and mol2.

Examples

name
res.num
atom1.name